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Acta Cryst. (2008). E64, o1902-o1903    [ doi:10.1107/S1600536808027888 ]

3-O-Benzhydryl-2,5-dideoxy-2,5-imino-2-C-methyl-L-lyxono-1,4-lactone

F. P. da Cruz, K. V. Booth, G. W. J. Fleet and D. J. Watkin

Abstract top

The title bicyclic lactone, C19H19NO3, is an intermediate in the synthesis of chiral [alpha]-methylprolines and branched C-methyl pyrrolidines; the absolute configuration was determined by the use of D-erythronolactone as the starting material. It exhibits no unusual crystal packing features, and each molecule acts as a donor and acceptor for one C-H...O hydrogen bond.

Comment top

Carbon-branched sugar lactones have hitherto been rarely used for the synthesis of enantiopure chiral targets (Monneret & Florent, 1994; Ireland et al., 1983). 2-C-Methyl-D-ribonolactone has become readily available in large amounts (Hotchkiss et al., 2007a) and has been used in the synthesis of branched α-C-nucleosides (Dukhan et al., 2005), 4-C-methylpentuloses (Rao et al., 2008) and branched imino sugars (Hotchkiss et al., 2007b). Derivatives of 2-C-methyl-D-arabinonolactone, such as 2, are accessible from D-erythronolactone 1 by addition of methyl magnesium bromide followed by further reaction with sodium cyanide (Hotchkiss et al., 2006; Punzo et al., 2005a). The tertiary alcohol 2 may be efficiently converted into the ribo-azide 3, the structure of which has been confirmed by X-ray crystallographic analysis (Da Cruz et al., 2008; Punzo et al., 2005b). The relative stereochemistry of 4 is firmly established in this paper by X-ray crystallographic analysis and the absolute configuration is defined by the use of D-erythronolactone 1 as the starting material.

The title compound exhibits no unusual crystal packing features. Each molecule acts as a donor and acceptor for one hydrogen bond, forming chains approximately parallel to the a-axis. A suggested hydrogen bond [N7 - H1 - O10] has been ignored in the packing diagram as it exceeds the limits of standard hydrogen bond length (2.52 Å)

Related literature top

For related literature, see: Monneret & Florent (1994); Ireland et al. (1983); Hotchkiss et al. (2006, 2007a,b); Dukhan et al. (2005); Rao et al. (2008); Punzo et al. (2005a,b); Da Cruz et al. (2008); Larson (1970); Prince (1982); Watkin (1994).

Experimental top

The title compound was recrystallized from cyclohexane and diethyl ether: m.p. 116–118°C; [α]D21 -26.0 (c, 1.0 in MeCN).

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged. The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98, N—H in the range 0.86–0.89 N—H to 0.86 O—H = 0.82 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

Computing details top

Data collection: COLLECT (Nonius, 1997-2001).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. Synthetic scheme.
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 3] Fig. 3. Packing diagram showing hydrogen bonded chains running parallel to the a-axis.
(I) top
Crystal data top
C19H19NO3F(000) = 656
Mr = 309.36Dx = 1.286 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 6711 reflections
a = 9.0336 (2) Åθ = 5–27°
b = 10.0498 (2) ŵ = 0.09 mm−1
c = 17.5941 (4) ÅT = 150 K
V = 1597.30 (6) Å3Block, colourless
Z = 40.30 × 0.25 × 0.25 mm
Data collection top
Nonius KappaCCD area-detector
diffractometer		1411 reflections with I > 2σ(I)
graphiteRint = 0.053
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −11→11
Tmin = 0.94, Tmax = 0.98k = −13→12
25603 measured reflectionsl = −22→22
2071 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.029 Method, part 1, Chebychev polynomial, (Watkin, 1994) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)]
where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 16.5 25.4 13.4 3.97
wR(F2) = 0.101(Δ/σ)max = 0.000186
S = 0.86Δρmax = 0.21 e Å−3
2071 reflectionsΔρmin = −0.21 e Å−3
212 parametersExtinction correction: Larson (1970), Equation 22
0 restraintsExtinction coefficient: 420 (70)
Primary atom site location: structure-invariant direct methods
Crystal data top
C19H19NO3V = 1597.30 (6) Å3
Mr = 309.36Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 9.0336 (2) ŵ = 0.09 mm−1
b = 10.0498 (2) ÅT = 150 K
c = 17.5941 (4) Å0.30 × 0.25 × 0.25 mm
Data collection top
Nonius KappaCCD area-detector
diffractometer		2071 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		1411 reflections with I > 2σ(I)
Tmin = 0.94, Tmax = 0.98Rint = 0.053
25603 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.029H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.101Δρmax = 0.21 e Å−3
S = 0.86Δρmin = −0.21 e Å−3
2071 reflectionsAbsolute structure: ?
212 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.68597 (16)0.81026 (14)0.31734 (9)0.0272
C20.6994 (2)0.69016 (19)0.27608 (12)0.0242
C30.7190 (3)0.5647 (2)0.32511 (13)0.0286
O40.76321 (17)0.46691 (14)0.26720 (9)0.0310
C50.8514 (3)0.5332 (2)0.21745 (12)0.0301
C60.8569 (2)0.6776 (2)0.24385 (12)0.0281
N70.9525 (2)0.6653 (2)0.31282 (12)0.0325
C80.8577 (3)0.5979 (2)0.37011 (13)0.0337
C90.9106 (3)0.7768 (3)0.18667 (15)0.0392
O100.9132 (2)0.47855 (18)0.16574 (10)0.0420
C110.5358 (2)0.8483 (2)0.33392 (12)0.0251
C120.5418 (2)0.9877 (2)0.36769 (12)0.0266
C130.6550 (3)1.0751 (2)0.34846 (13)0.0315
C140.6565 (3)1.2033 (2)0.37762 (14)0.0370
C150.5459 (3)1.2459 (2)0.42665 (15)0.0406
C160.4328 (3)1.1595 (2)0.44577 (15)0.0402
C170.4305 (3)1.0309 (2)0.41629 (13)0.0344
C180.4604 (2)0.74727 (19)0.38447 (11)0.0253
C190.5194 (3)0.7164 (2)0.45543 (12)0.0322
C200.4554 (3)0.6179 (3)0.50012 (13)0.0405
C210.3303 (3)0.5504 (2)0.47385 (16)0.0422
C220.2698 (3)0.5832 (2)0.40451 (16)0.0397
C230.3342 (3)0.6812 (2)0.35977 (13)0.0312
H210.62170.67910.23670.0282*
H310.63440.53650.35480.0341*
H810.83350.65810.41260.0399*
H820.90620.51760.38800.0400*
H911.01250.76350.17450.0585*
H920.90020.86650.20830.0596*
H930.85090.77210.14110.0587*
H1110.48140.85230.28510.0297*
H1310.73061.04740.31580.0374*
H1410.73371.26280.36360.0445*
H1510.54851.33150.44720.0487*
H1610.35641.18730.47880.0478*
H1710.35270.97330.42990.0420*
H1910.60400.76420.47310.0384*
H2010.49690.59680.54710.0498*
H2110.28660.48320.50360.0514*
H2210.18480.53710.38610.0482*
H2310.29130.70170.31180.0394*
H10.980 (4)0.748 (3)0.3251 (17)0.0433*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0237 (7)0.0228 (7)0.0350 (7)0.0012 (6)0.0009 (6)−0.0054 (6)
C20.0247 (9)0.0202 (9)0.0278 (9)−0.0005 (8)0.0007 (8)−0.0031 (8)
C30.0329 (11)0.0225 (9)0.0303 (10)0.0008 (8)0.0044 (9)−0.0034 (8)
O40.0330 (8)0.0242 (7)0.0359 (8)0.0010 (6)0.0024 (7)−0.0046 (7)
C50.0280 (10)0.0300 (10)0.0324 (10)0.0045 (9)−0.0011 (9)−0.0022 (9)
C60.0243 (10)0.0261 (9)0.0340 (10)0.0013 (8)0.0015 (8)−0.0012 (9)
N70.0264 (9)0.0306 (9)0.0404 (10)0.0011 (8)−0.0073 (8)−0.0026 (8)
C80.0375 (12)0.0306 (11)0.0331 (11)0.0063 (10)−0.0040 (10)0.0005 (9)
C90.0358 (12)0.0361 (12)0.0457 (13)−0.0005 (10)0.0122 (11)0.0078 (11)
O100.0462 (10)0.0399 (9)0.0398 (9)0.0087 (8)0.0086 (8)−0.0084 (8)
C110.0224 (9)0.0270 (9)0.0260 (9)0.0031 (8)−0.0017 (8)−0.0001 (8)
C120.0285 (10)0.0247 (9)0.0265 (9)0.0045 (8)−0.0011 (8)0.0008 (8)
C130.0307 (11)0.0267 (10)0.0372 (11)0.0034 (9)0.0025 (10)0.0025 (9)
C140.0385 (12)0.0246 (10)0.0478 (13)−0.0016 (10)0.0034 (11)0.0045 (10)
C150.0496 (15)0.0239 (11)0.0482 (14)0.0065 (10)0.0007 (12)−0.0049 (9)
C160.0421 (14)0.0335 (12)0.0452 (13)0.0062 (11)0.0100 (11)−0.0051 (10)
C170.0361 (12)0.0289 (11)0.0383 (12)0.0023 (10)0.0079 (10)−0.0004 (9)
C180.0265 (10)0.0230 (9)0.0265 (10)0.0029 (8)0.0018 (9)−0.0030 (8)
C190.0408 (13)0.0287 (10)0.0272 (10)0.0053 (11)−0.0017 (10)−0.0039 (8)
C200.0570 (16)0.0362 (12)0.0283 (10)0.0138 (11)0.0069 (12)0.0020 (10)
C210.0474 (14)0.0292 (11)0.0501 (14)0.0055 (11)0.0209 (13)0.0051 (10)
C220.0348 (12)0.0299 (11)0.0544 (15)−0.0019 (10)0.0093 (12)−0.0035 (11)
C230.0284 (10)0.0295 (10)0.0356 (10)0.0009 (8)0.0004 (9)−0.0038 (9)
Geometric parameters (Å, °) top
O1—C21.414 (2)C12—C131.390 (3)
O1—C111.439 (2)C12—C171.389 (3)
C2—C31.538 (3)C13—C141.387 (3)
C2—C61.537 (3)C13—H1310.935
C2—H210.992C14—C151.388 (4)
C3—O41.471 (2)C14—H1410.951
C3—C81.519 (3)C15—C161.382 (4)
C3—H310.968C15—H1510.934
O4—C51.358 (3)C16—C171.393 (3)
C5—C61.524 (3)C16—H1610.945
C5—O101.200 (3)C17—H1710.941
C6—N71.495 (3)C18—C191.393 (3)
C6—C91.497 (3)C18—C231.389 (3)
N7—C81.486 (3)C19—C201.390 (4)
N7—H10.89 (3)C19—H1910.954
C8—H810.986C20—C211.397 (4)
C8—H820.971C20—H2010.932
C9—H910.955C21—C221.377 (4)
C9—H920.983C21—H2110.942
C9—H930.968C22—C231.389 (4)
C11—C121.523 (3)C22—H2210.954
C11—C181.512 (3)C23—H2310.952
C11—H1110.990
C2—O1—C11114.34 (15)C12—C11—C18113.84 (17)
O1—C2—C3114.94 (16)O1—C11—H111107.6
O1—C2—C6109.83 (16)C12—C11—H111108.5
C3—C2—C691.88 (16)C18—C11—H111108.3
O1—C2—H21113.2C11—C12—C13120.81 (19)
C3—C2—H21112.4C11—C12—C17120.2 (2)
C6—C2—H21112.8C13—C12—C17119.0 (2)
C2—C3—O4100.99 (16)C12—C13—C14120.3 (2)
C2—C3—C8101.98 (17)C12—C13—H131119.9
O4—C3—C8106.51 (17)C14—C13—H131119.8
C2—C3—H31116.9C13—C14—C15120.6 (2)
O4—C3—H31113.0C13—C14—H141119.7
C8—C3—H31115.7C15—C14—H141119.7
C3—O4—C5106.11 (16)C14—C15—C16119.4 (2)
O4—C5—C6106.84 (17)C14—C15—H151120.5
O4—C5—O10122.5 (2)C16—C15—H151120.2
C6—C5—O10130.6 (2)C15—C16—C17120.2 (2)
C2—C6—C599.24 (16)C15—C16—H161120.3
C2—C6—N7104.02 (17)C17—C16—H161119.5
C5—C6—N7100.82 (17)C16—C17—C12120.6 (2)
C2—C6—C9119.55 (18)C16—C17—H171119.2
C5—C6—C9116.07 (19)C12—C17—H171120.3
N7—C6—C9114.42 (19)C11—C18—C19120.3 (2)
C6—N7—C8104.77 (16)C11—C18—C23120.47 (19)
C6—N7—H1106 (2)C19—C18—C23119.2 (2)
C8—N7—H1115 (2)C18—C19—C20120.4 (2)
C3—C8—N7102.82 (18)C18—C19—H191119.1
C3—C8—H81110.3C20—C19—H191120.5
N7—C8—H81111.3C19—C20—C21119.7 (2)
C3—C8—H82111.0C19—C20—H201119.8
N7—C8—H82109.7C21—C20—H201120.5
H81—C8—H82111.3C20—C21—C22119.9 (2)
C6—C9—H91111.7C20—C21—H211120.3
C6—C9—H92108.6C22—C21—H211119.9
H91—C9—H92107.9C21—C22—C23120.4 (3)
C6—C9—H93110.2C21—C22—H221120.3
H91—C9—H93110.1C23—C22—H221119.3
H92—C9—H93108.2C18—C23—C22120.4 (2)
O1—C11—C12106.90 (17)C18—C23—H231120.5
O1—C11—C18111.45 (16)C22—C23—H231119.1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C20—H201···O10i0.932.363.293 (3)174
N7—H1···O10ii0.89 (2)2.52 (3)3.395 (3)168
Symmetry codes: (i) −x+3/2, −y+1, z+1/2; (ii) −x+2, y+1/2, −z+1/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C20—H201···O10i0.932.363.293 (3)174
Symmetry codes: (i) −x+3/2, −y+1, z+1/2.
Acknowledgements top

Financial support (to FPC) provided by the Fundacao para a Ciencia e Tecnologia of Portugal is gratefully acknowledged. We also thank the Oxford University Crystallography Service for use of the instruments.

references
References top

Altomare, A., Cascarano, G., Giacovazzo, G., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.

Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.

Da Cruz, F. P., Horne, G. & Fleet, G. W. J. (2008). In preparation.

Dukhan, D., Bosc, E., Peyronnet, J., Storer, R. & Gosselin, G. (2005). Nucleosides, Nucleotides Nucleic Acids, 24, 577–580.

Hotchkiss, D. J., Jenkinson, S. F., Storer, R., Heinz, T. & Fleet, G. W. J. (2006). Tetrahedron Lett. 47, 315–318.

Hotchkiss, D. J., Kato, A., Odell, B., Claridge, T. D. W. & Fleet, G. W. J. (2007b). Tetrahedron Asymmetry, 18, 500–512.

Hotchkiss, D. J., Soengas, R., Booth, K. V., Weymouth-Wilson, A. C., Eastwick-Field, V. & Fleet, G. W. J. (2007a). Tetrahedron Lett. 48, 517–520.

Ireland, R. E., Courtney, L. & Fitzsimmons, B. J. (1983). J. Org. Chem. 48, 5186–5198.

Larson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 291–294. Copenhagen: Munksgaard.

Monneret, C. & Florent, J. C. (1994). Synlett, pp. 305–318.

Nonius (1997–2001). COLLECT. Nonius BV, Delft, The Netherlands.

Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.

Prince, E. (1982). Mathematical Techniques in Crystallography and Materials Science. Springer-Verlag, New York.

Punzo, F., Watkin, D. J., Jenkinson, S. F., Cruz, F. P. & Fleet, G. W. J. (2005b). Acta Cryst. E61, o511–o512.

Punzo, F., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2005a). Acta Cryst. E61, o127–o129.

Rao, D., Yoshihara, A., Gullapalli, P., Morimoto, K., Takata, G., da Cruz, F. P., Jenkinson, S. F., Wormald, M. R., Dwek, R. A., Fleet, G. W. J. & Izumori, K. (2008). Tetrahedron Lett. 49, 3316–3321.

Watkin, D. (1994). Acta Cryst. A50, 411–437.

Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, UK.